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vg
tools for working with variation graphs
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This is the complete list of members for vg::VCFTraversalFinder, including all inherited members.
| brute_force_alt_traversals(const Snarl &site, const vector< vcflib::Variant * > &site_variants, path_handle_t ref_path, step_handle_t start_step, step_handle_t end_step, vector< pair< SnarlTraversal, vector< int > > > &output_traversals) | vg::VCFTraversalFinder | protected |
| check_max_trav_cutoff(const vector< vector< int > > &alleles) | vg::VCFTraversalFinder | protected |
| create_variant_index(vcflib::VariantCallFile &vcf, FastaReference *ref_fasta=nullptr, FastaReference *ins_fasta=nullptr) | vg::VCFTraversalFinder | protected |
| delete_variant_index() | vg::VCFTraversalFinder | protected |
| find_allele_traversals(Snarl site) | vg::VCFTraversalFinder | |
| find_traversals(const Snarl &site) | vg::VCFTraversalFinder | virtual |
| vg::TraversalFinder::find_traversals(const handle_t &snarl_start, const handle_t &snarl_end) | vg::TraversalFinder | inlinevirtual |
| get_alt_path(vcflib::Variant *site_variant, int allele, path_handle_t ref_path) | vg::VCFTraversalFinder | protected |
| get_alt_traversal(const Snarl &site, const vector< vcflib::Variant * > &site_variants, path_handle_t ref_path, step_handle_t start_step, step_handle_t end_step, const vector< int > &haplotype) | vg::VCFTraversalFinder | protected |
| get_haplotype_alt_contents(const vector< vcflib::Variant * > &site_variants, const vector< int > &haplotype, path_handle_t ref_path) | vg::VCFTraversalFinder | protected |
| get_pruned_alt_alleles(const Snarl &site, const vector< vcflib::Variant * > &site_variants, path_handle_t ref_path) | vg::VCFTraversalFinder | protected |
| get_variants_in_site(const Snarl &site) | vg::VCFTraversalFinder | |
| graph | vg::VCFTraversalFinder | protected |
| include_endpoints | vg::VCFTraversalFinder | protected |
| max_deletion_scan_nodes | vg::VCFTraversalFinder | protected |
| max_prune_iterations | vg::VCFTraversalFinder | protected |
| max_traversal_cutoff | vg::VCFTraversalFinder | protected |
| node_to_variant | vg::VCFTraversalFinder | protected |
| path_finder | vg::VCFTraversalFinder | protected |
| scan_for_deletion(vcflib::Variant *var, int allele, path_handle_t ref_path, step_handle_t first_path_step, step_handle_t last_path_step) | vg::VCFTraversalFinder | protected |
| skip_alt | vg::VCFTraversalFinder | protected |
| snarl_manager | vg::VCFTraversalFinder | protected |
| step_in_path(handle_t handle, path_handle_t path_handle) const | vg::VCFTraversalFinder | protected |
| VCFTraversalFinder(const PathHandleGraph &graph, SnarlManager &snarl_manager, vcflib::VariantCallFile &vcf, const vector< string > &ref_path_names={}, FastaReference *fasta_ref=nullptr, FastaReference *ins_ref=nullptr, function< bool(const SnarlTraversal &, int)> skip_alt=nullptr, size_t max_traversal_cutoff=50000) | vg::VCFTraversalFinder | |
| ~TraversalFinder()=default | vg::TraversalFinder | virtual |
| ~VCFTraversalFinder() | vg::VCFTraversalFinder | virtual |
1.8.17